Add warning messages for detected invalid alignments

[rsem.git] / PairedEndModel.h

diff --git a/PairedEndModel.h b/PairedEndModel.h
index 70d14c9de9a97680eb9a683715f887a1d2a1e16f..575344c348c6aa1783b66e98a3d760484ec27e22 100644 (file)
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -10,6 +10,7 @@
 #include<sstream>
 
 #include "utils.h"
+#include "my_assert.h"
 #include "Orientation.h"
 #include "LenDist.h"
 #include "RSPD.h"
@@ -99,7 +100,15 @@ public:
                int fpos = (dir == 0 ? pos : totLen - pos - insertLen); // the aligned position reported in SAM file, should be a coordinate in forward strand
                int effL = std::min(fullLen, totLen - insertLen + 1);
                
-               assert(fpos >= 0 && fpos + insertLen <= totLen && insertLen <= totLen);
+               general_assert(fpos >= 0, "The alignment of fragment " + read.getName() + " to transcript " + itos(sid) + " starts at " + itos(fpos) + \
+                               " from the forward direction, which should be a non-negative number! " + \
+                               "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(fpos + insertLen <= totLen,"Fragment " + read.getName() + " is hung over the end of transcript " + itos(sid) + "! " \
+                               + "It is possible that the aligner you use gave different read lengths for a same read in SAM file.");
+               general_assert(insertLen <= totLen, "Fragment " + read.getName() + " has length " + itos(insertLen) + ", but it is aligned to transcript " \
+                               + itos(sid) + ", whose length (" + itos(totLen) + ") is shorter than the fragment's length!");
+
+
                if (fpos >= fullLen || ref.getMask(fpos)) return 0.0; // For paired-end model, fpos is the seedPos
 
                prob = ori->getProb(dir) * gld->getAdjustedProb(insertLen, totLen) *